Abstract
Automated methods for NMR structure determination of proteins are continuously becoming more robust. However, current methods addressing larger, more complex targets rely on analyzing 6-10 complementary spectra, suggesting the need for alternative approaches. Here, we describe 4D-CHAINS/autoNOE-Rosetta, a complete pipeline for NOE-driven structure determination of medium- to larger-sized proteins. The 4D-CHAINS algorithm analyzes two 4D spectra recorded using a single, fully protonated protein sample in an iterative ansatz where common NOEs between different spin systems supplement conventional through-bond connectivities to establish assignments of sidechain and backbone resonances at high levels of completeness and with a minimum error rate. The 4D-CHAINS assignments are then used to guide automated assignment of long-range NOEs and structure refinement in autoNOE-Rosetta. Our results on four targets ranging in size from 15.5 to 27.3 kDa illustrate that the structures of proteins can be determined accurately and in an unsupervised manner in a matter of days.
[NMR paper] Automated protein structure determination by NMR.
Automated protein structure determination by NMR.
Related Articles Automated protein structure determination by NMR.
J Biomol NMR. 2015 Jul 21;
Authors: Rosato A, Billeter M
PMID: 26195076
[NMR paper] Automated structure determination from NMR spectra.
Automated structure determination from NMR spectra.
Automated structure determination from NMR spectra.
Methods Mol Biol. 2015;1261:303-29
Authors: Schmidt E, Güntert P
Abstract
Three-dimensional structures of proteins in solution can be calculated on the basis of conformational restraints derived from NMR measurements. This chapter gives an overview of the computational methods for NMR protein structure analysis highlighting recent automated methods for the assignment of NMR spectra, the collection of conformational restraints,...
[NMR paper] Automated protein NMR resonance assignments.
Automated protein NMR resonance assignments.
Related Articles Automated protein NMR resonance assignments.
Proc IEEE Comput Soc Bioinform Conf. 2003;2:197-208
Authors: Wan X, Xu D, Slupsky CM, Lin G
NMR resonance peak assignment is one of the key steps in solving an NMR protein structure. The assignment process links resonance peaks to individual residues of the target protein sequence, providing the prerequisite for establishing intra- and inter-residue spatial relationships between atoms. The assignment process is tedious and time-consuming,...
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[NMR paper] Automated protein fold determination using a minimal NMR constraint strategy.
Automated protein fold determination using a minimal NMR constraint strategy.
Related Articles Automated protein fold determination using a minimal NMR constraint strategy.
Protein Sci. 2003 Jun;12(6):1232-46
Authors: Zheng D, Huang YJ, Moseley HN, Xiao R, Aramini J, Swapna GV, Montelione GT
Determination of precise and accurate protein structures by NMR generally requires weeks or even months to acquire and interpret all the necessary NMR data. However, even medium-accuracy fold information can often provide key clues about protein evolution...
Automated NMR resonance assignments and structure determination using a minimal set of 4D spectra.
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